Abstract
Guanine (G)-rich DNA readily forms four-stranded quadruplexes in vitro, but evidence for their participation in genome regulation is limited. We have identified a quadruplex-binding protein, Lia3, that controls the boundaries of germline-limited, internal eliminated sequences (IESs) of Tetrahymena thermophila. Differentiation of this ciliate’s somatic genome requires excision of thousands of IESs, targeted for removal by small-RNA-directed heterochromatin formation. In cells lacking LIA3 (ΔLIA3), the excision of IESs bounded by specific G-rich polypurine tracts was impaired and imprecise, whereas the removal of IESs without such controlling sequences was unaffected. We found that oligonucleotides containing these polypurine tracts formed parallel G-quadruplex structures that are specifically bound by Lia3. The discovery that Lia3 binds G-quadruplex DNA and controls the accuracy of DNA elimination at loci with specific G-tracts uncovers an unrecognized potential of quadruplex structures to regulate chromosome organization.
Highlights
Ciliates maintain distinct germline and somatic genomes that are partitioned into different nuclei, called micro- and macronuclei, respectively [1]
We show that the Lia3 protein binds the M internal eliminated sequences (IESs) A5G5 boundary determinant when it adopts a non-canonical Guanine quadruplex (G4 DNA) structure
In our search for proteins that are important for the differentiation of the somatic genome, we identified candidates, including Lia3, that are expressed during conjugation and localize to developing macronuclei [13]
Summary
Ciliates maintain distinct germline and somatic genomes that are partitioned into different nuclei, called micro- and macronuclei, respectively [1]. The subsequent differentiation of the somatic genome involves massive genome reorganization, which includes fragmentation of the chromosomes and elimination of a large fraction of the germline-derived sequence. In the ciliate Tetrahymena thermophila, more than 6,000 dispersed loci, comprising nearly one-third of the genome, are eliminated [2]. These internal eliminated sequences (IESs) consist of both unique and repetitive sequences that are most likely evolutionarily derived from the movement of transposable elements. DNA elimination serves as an effective genome surveillance mechanism that silences these potentially deleterious sequences by removing them from the transcribed nucleus [reviewed in 3]
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